This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

2b89

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 08:25, 14 June 2023

Structural basis for molecular recognition in an affibody:affibody complex

Structural highlights

2b89 is a 1 chain structure with sequence from Staphylococcus aureus. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

Q70AB8_STAAU

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

Affibody molecules constitute a class of engineered binding proteins based on the 58-residue three-helix bundle Z domain derived from staphylococcal protein A (SPA). Affibody proteins are selected as binders to target proteins by phage display of combinatorial libraries in which typically 13 side-chains on the surface of helices 1 and 2 in the Z domain have been randomized. The Z(Taq):anti-Z(Taq) affibody-affibody complex, consisting of Z(Taq), originally selected as a binder to Taq DNA polymerase, and anti-Z(Taq), selected as binder to Z(Taq), is formed with a dissociation constant K(d) approximately 100 nM. We have determined high-precision solution structures of free Z(Taq) and anti-Z(Taq), and the Z(Taq):anti-Z(Taq) complex under identical experimental conditions (25 degrees C in 50 mM NaCl with 20 mM potassium phosphate buffer at pH 6.4). The complex is formed with helices 1 and 2 of anti-Z(Taq) in perpendicular contact with helices 1 and 2 of Z(Taq). The interaction surface is large ( approximately 1670 A(2)) and unusually non-polar (70 %) compared to other protein-protein complexes. It involves all varied residues on anti-Z(Taq), most corresponding (Taq DNA polymerase binding) side-chains on Z(Taq), and several additional side-chain and backbone contacts. Other notable features include a substantial rearrangement (induced fit) of aromatic side-chains in Z(Taq) upon binding, a close contact between glycine residues in the two subunits that might involve aliphatic glycine Halpha to backbone carbonyl hydrogen bonds, and four hydrogen bonds made by the two guanidinium N(eta)H(2) groups of an arginine side-chain. Comparisons of the present structure with other data for affibody proteins and the Z domain suggest that intrinsic binding properties of the originating SPA surface might be inherited by the affibody binders. A thermodynamic characterization of Z(Taq) and anti-Z(Taq) is presented in an accompanying paper.

Structural basis for molecular recognition in an affibody:affibody complex.,Lendel C, Dogan J, Hard T J Mol Biol. 2006 Jun 23;359(5):1293-304. Epub 2006 May 6. PMID:16750222^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Lendel C, Dogan J, Hard T. Structural basis for molecular recognition in an affibody:affibody complex. J Mol Biol. 2006 Jun 23;359(5):1293-304. Epub 2006 May 6. PMID:16750222 doi:10.1016/j.jmb.2006.04.043

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2b89"

Categories: Large Structures | Staphylococcus aureus | Dogan J | Hard T | Lendel C

@@ Line 1: / Line 1: @@
 ==Structural basis for molecular recognition in an affibody:affibody complex==
-<StructureSection load='2b89' size='340' side='right'caption='[[2b89]], [[NMR_Ensembles_of_Models | 40 NMR models]]' scene=''>
+<StructureSection load='2b89' size='340' side='right'caption='[[2b89]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2b89]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"micrococcus_aureus"_(rosenbach_1884)_zopf_1885 "micrococcus aureus" (rosenbach 1884) zopf 1885]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2B89 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2B89 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2b89]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2B89 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2B89 FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2b87|2b87]], [[2b88|2b88]]</div></td></tr>
+</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2b89 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2b89 OCA], [https://pdbe.org/2b89 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2b89 RCSB], [https://www.ebi.ac.uk/pdbsum/2b89 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2b89 ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2b89 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2b89 OCA], [https://pdbe.org/2b89 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2b89 RCSB], [https://www.ebi.ac.uk/pdbsum/2b89 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2b89 ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q70AB8_STAAU Q70AB8_STAAU]
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 31: / Line 32: @@
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Dogan, J]]
+[[Category: Staphylococcus aureus]]
-[[Category: Hard, T]]
+[[Category: Dogan J]]
-[[Category: Lendel, C]]
+[[Category: Hard T]]
-[[Category: Affibody]]
+[[Category: Lendel C]]
-[[Category: Induced fit]]
-[[Category: Molecular recognition]]
-[[Category: Nmr spectroscopy]]
-[[Category: Protein binding]]
-[[Category: Protein engineering]]
-[[Category: Protein-protein interaction]]

2b89

From Proteopedia

Revision as of 08:25, 14 June 2023

Structural basis for molecular recognition in an affibody:affibody complex

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox